Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

Fleishman, Sarel J.; Whitehead, Timothy A.; Ekiert, D.C.; Dreyfus, Cyrille; Corn, Jacob E.; Strauch, Eva-Maria; Wilson, Ian A.; Baker, David

doi:10.1126/science.1202617

Cited by 549 publications

(610 citation statements)

References 20 publications

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“…de novo design | protein design | ideal protein | control protein shape P rotein design holds promise for applications ranging from therapeutics to biomaterials, with recent progress in designing small molecule binding proteins (1,2), inhibitors of protein-protein interactions (3,4), and self-assembling nanomaterials (5)(6)(7). Most of these efforts have repurposed naturally occurring scaffolds, which are likely not optimal starting points for creating new functions because they generally contain sequence and structural idiosyncrasies that arose during evolutionary optimization for their natural functions (8).…”

mentioning

confidence: 99%

Control over overall shape and size in de novo designed proteins

Lin

Koga

Tatsumi-Koga

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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155

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We recently described general principles for designing ideal protein structures stabilized by completely consistent local and nonlocal interactions. The principles relate secondary structure patterns to tertiary packing motifs and enable design of different protein topologies. To achieve fine control over protein shape and size within a particular topology, we have extended the design rules by systematically analyzing the codependencies between the lengths and packing geometry of successive secondary structure elements and the backbone torsion angles of the loop linking them. We demonstrate the control afforded by the resulting extended rule set by designing a series of proteins with the same fold but considerable variation in secondary structure length, loop geometry, β-strand registry, and overall shape. Solution NMR structures of four designed proteins for two different folds show that protein shape and size can be precisely controlled within a given protein fold. These extended design principles provide the foundation for custom design of protein structures performing desired functions.de novo design | protein design | ideal protein | control protein shape P rotein design holds promise for applications ranging from therapeutics to biomaterials, with recent progress in designing small molecule binding proteins (1, 2), inhibitors of protein-protein interactions (3, 4), and self-assembling nanomaterials (5-7). Most of these efforts have repurposed naturally occurring scaffolds, which are likely not optimal starting points for creating new functions because they generally contain sequence and structural idiosyncrasies that arose during evolutionary optimization for their natural functions (8). Robust design of new functional proteins would be considerably enabled by the capability of precisely designing from scratch arbitrary protein structures.We previously described general principles that allowed the de novo design of ideal protein structures with five different folds (9). In this paper, we focus on the "variations on a theme" problem of precisely controlling structural variation within the same fold. To achieve such control, we begin by characterizing the coupling between loop backbone geometry and the packing of the flanking secondary elements. We then use the resulting extended set of design principles to systematically vary structure for two different folds and describe the experimental characterization of five of these de novo designed proteins. ResultsLocal Structure Building Blocks. The design rules described in our previous paper relate the packing orientation of ββ-, βα-, and αβ-units to the length of the loop connecting them (9). Here, we begin by extending these rules to the level of specific loop conformations to allow more detailed control over local geometry and overall protein topology.It is convenient to describe protein local geometry by using the ABEGO (10) alphabet illustrated in Fig. 1A. "A" indicates the alpha region of the Ramachandran plot (11); "B," the beta region; "G" and "E", the po...

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mentioning

confidence: 99%

Control over overall shape and size in de novo designed proteins

Lin

Koga

Tatsumi-Koga

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

126

155

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“…The crowd-sourced protein folding and design 'games' undertaken by the global Foldit community to identify inhibitors that bind and inhibit the 1918 pandemic influenza virus have shown that distributed problem solving in medicine and health can be very powerful (Fleishman et al 2011).…”

Section: Research Agendas For Global Healthmentioning

confidence: 99%

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Carothers

2013

Syst Synth Biol

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Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commerciallyimportant applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.

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“…We have tested two assay stack formats utilizing two different binders. The first is an HA stem-region binder, which was originally reported by Fleishman et al [14] and has since been optimized by Whitehead et al [15]. The second protein is an HA head-region binder, which is under development with a publication in progress.…”

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confidence: 99%

Development of a paper-based diagnostic for influenza detection

Holstein

Bennett

Strauch

et al. 2014

2014 IEEE Healthcare Innovation Conference (HIC)

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Abstract-The development of novel paper-based diagnostic tests has surged in recent years, due to the suitability of these tests for use at the point of care. These emerging paper-based tests retain the low cost and ease of use of traditional lateral flow tests, while offering increased sophistication and capabilities that approach those of traditional microfluidic devices. Here, we report on the development of a novel paperbased test for the diagnosis of influenza, commonly known as the flu. Influenza is a ubiquitously occurring infection, affecting 5-20% of Americans and resulting in an average of 23,000 deaths in the U.S., and up to 500,000 deaths globally, each year. Despite its prevalence, the diagnosis of influenza remains unsatisfactory, especially at the point of care. In particular, lateral flow tests for influenza suffer from poor sensitivity and provide only limited information about the infecting flu virus. Point-of-care testing of influenza therefore stands to benefit substantially from improved technology. To this end, we have developed two different versions of a paper-based flu assay, both using computationally designed affinity proteins, or "binders," that bind to the influenza hemagglutinin (HA) protein. One version of the assay utilizes an HA stem-region binder and the other an HA head-region binder. With these assays, we demonstrate the detection of clinically relevant concentrations of recombinant HA and intact influenza virus, as well as the translation of this paper-based system to a twodimensional paper network (2DPN) folding card device.

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Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

Cited by 549 publications

References 20 publications

Control over overall shape and size in de novo designed proteins

Control over overall shape and size in de novo designed proteins

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Development of a paper-based diagnostic for influenza detection

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